I am using galaxy platform to run Bowtie 2. I have illumina paired end reads (file#1 and file#2) in two separate fastq files. I am trying to map the reads against the host genome (built in) to filter out any host gene sequences using Bowtie 2.I am expecting to get unaligned paired end reads where i will have file#1 and file#2. But in the galaxy workflow the output files are showing up as "output_unaligned_reads_l" and "output_unaligned_reads_r". I am not sure what does this "l" and "r" files mean? Is it referring to file#1 and file#2 or it is combining the two files in one format?
In such case, how do i get unaligned paired end reads (separate files) in this case? In the next step, i will need to use the unaligned paired end files to map against another reference AMR database using bowtie2.
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Question: Bowtie 2 output read
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jahan036 • 0 wrote:
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modified 13 months ago
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Jennifer Hillman Jackson ♦ 25k
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13 months ago by
jahan036 • 0
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Jennifer Hillman Jackson ♦ 25k wrote:
Hello,
The primary output is a BAM dataset. This is where your mapping results are.
There are options on the tool form to output aligned/unaligned reads in fastq format. If selected, output_unaligned_reads_l represents the unaligned forward reads (first fastq entered on the tool form) and output_unaligned_reads_r represents the unaligned reverse reads (second fastq entered on the tool form).
These can then be used as separate paired-end inputs for the next mapping run.
Hope that helps! Jen, Galaxy team
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